Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA polymerase delta catalytic subunit.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g2005 g2005.t2 TSS g2005.t2 14376314 14376314
chr_3 g2005 g2005.t2 isoform g2005.t2 14377305 14379865
chr_3 g2005 g2005.t2 exon g2005.t2.exon1 14377305 14379865
chr_3 g2005 g2005.t2 cds g2005.t2.CDS1 14377509 14379818
chr_3 g2005 g2005.t2 TTS g2005.t2 14379883 14379883

Sequences

>g2005.t2 Gene=g2005 Length=2561
AGAGTAAAAGGAACCAAGCCTGAACCTGAAAGCCGTTGCCAATTAGAAGTTGATGTTGCA
TATGACAAATTTATTGCACACGAGCCAGAAGGAGAATGGTCAAAAGTAGCACCATTTAGA
ATTCTCAGTTTCGATATAGAATGTGCCGGCAGAAAAGGTATATTTCCAGAACCGAAATAC
GATCCTGTCATTCAAATTGCAAACATGGTTATGAGACAAGGCGAAAAAGAACCGTTCTTA
AGAAATGTATTTACTTTAGATACGTGCGCACCAATTGTAGGATCTCAAGTGCTCAGTTAT
AAGAAAGAAACAGAATTACTTGATGCTTGGAGTGCTTTTGTTCGTGAACTTGATCCTGAT
ATCATTACTGGTTATAATATTAATAATTTTGATGTACCATATCTTATCGAAAGAGCCAAA
CATCTAAAAGTCGATAAATTTGTTTATCTTGGACGAATGAAAGATGTCAAATCGGTCATA
AAAGAATCAGTTATTCAATCTAAACAAATGGGACGACGTGAAAACAAGCAAGTCAATTTT
GAAGGACGTGTTCCTTTCGATTTGCTATTTGTGCTCTTCCGCGATTACAAACTCCGATCA
TATACATTGAACGCTGTCAGTTATCACTTTCTGCAAGAACAAAAAGAAGATGTACATCAC
AGCATAATCTCAGATCTTCAAAATGGCACTGAACAAACACGTCGACGTCTTGCTATGTAT
TGTCTTAAAGATGCATATTTGCCATTGAGATTACTCAACAAATTAATGTGTATCGTCAAC
TATATGGAAATGGCTCGTGTAACGGGAGTTTCATTGGCTAGTTTACTAACTCGTGGTCAA
CAAATCAAAGTTGTCAGTCAATTATTGAGAAAAGCACGTGATGCCGGATATTTGATTCCA
ACTTACACTAGTCAAGGTGGCGATAATGAACAATTTGAAGGAGCAACAGTTATTGAACCA
AAAAGAGGCTACTATTCAGTCCCAATCGCCACTCTCGATTTTGCTTCTCTATATCCATCA
ATCATGATGGCACATAATTTGTGTTACACAACATTGTTGAAACCATCGGACAGAAAAAAA
TTGGATTTAAAAGATGAAGATGTCACGCAAACACCAGCTGGAAATTTTTTTGTTAAACCA
AATGTCAGAAAAGGTCTTTTACCAGAAATTCTTGAATCTTTGCTCAGTGCACGTAAGAAA
GCCAAAGCCGATTTGAAATCAGAAACTGATCCATTTAAAAGAAGCGTTCTCGATGGTCGA
CAGCTTGCATTGAAAATTAGTGCCAATTCAGTTTATGGATTTACAGGTGCACAAGTAGGA
AAACTGCCTTGTTTAGAAATTTCTGGAAGTGTTACAGCTTATGGTCGTACAATGATTGAA
ATGACAAAGAATGAAGTAGAGAAAAAATATACTCTATCAAATGGTTATGATTCTGACGCT
TTTGTTATTTACGGAGATACTGATTCAGTTATGGTAAACTTTGGAACAGAATCGTTACCA
CGTGCGATGGAATTAGGAAGAGAAGCAGCTGAATTTGTTAGCGAAAAATTTATTAAACCA
ATCAAACTTGAATTCGAGAAAGTTTATTATCCTTATTTACTTATTAACAAGAAACGTTAT
GCTGGATTGTATTGGACAAAACCTGAAAATTATGATAAAATGGACTGCAAAGGTATTGAA
ACTGTTCGTCGTGATAATTCACCTCTTGTTGCAAATTTAATGAATACTTGCCTACAAAAA
CTTTTGATTGAGCGCAATCCAACAGAAGCTGTTGATTATGTCAAATCAATTATCTCAGAT
TTACTTTGTAATCGAATTGATATTTCACAGTTGGTCATCACAAAAGAATTAACAAAGCAT
GACTATGCTGCAAAACAAGCACACGTTGAGCTTGCTGCAAAAATGAAGAAAAGAGATCCT
GGAAATGCACCGAAACTTGGCGATCGTGTACCATATGTTATCACAGCATCTGCTAAAAGT
ACACCAGCATATCAAAAGGCAGAAGATCCTGTTTATGTACTTGAAAATAGCATTCCAATC
GACTTTCAATATTATCTCGATAATCAGCTCTCTAAACCATTATTGAGAATTTTTGAGCCA
ATTCTTGGAGATAAAGCAGAATCAATTTTACTTCGTGGTGATCATACTCGAACAAGAATG
GGTGGAACATCAAAAGTATCAGCATTAAGTGCATTTGTACAACGTAAAGAAACATGCATT
GGTTGTAAATCTGTATTGTCAGCTGATAGATCTAAAGGAGCCTTATGCCAGCATTGCGAG
ACAAAATCTGATGAAATTTATCAAAATGAGATTGTTCAACAATGTCAACTTGAAGAAAGA
TTTTCAAGATTATGGGCAGAATGTCAACGATGTCAAGGAGCTAGAAATGAAGAAGTCTTA
TGCACAAGTCGCGATTGTCCAATCTTTTATATGCGAACAAAAGTTAGAATGGACTTGGAT
ACACAAAATAAGAGAATTATGCGATTTGGCCTTTCTGCTATAAACAACTGGTAGTTTTCA
TTTATTTTAAAAATTCAATTTTATTATTTGCCAATAAAGAT

>g2005.t2 Gene=g2005 Length=769
MVMRQGEKEPFLRNVFTLDTCAPIVGSQVLSYKKETELLDAWSAFVRELDPDIITGYNIN
NFDVPYLIERAKHLKVDKFVYLGRMKDVKSVIKESVIQSKQMGRRENKQVNFEGRVPFDL
LFVLFRDYKLRSYTLNAVSYHFLQEQKEDVHHSIISDLQNGTEQTRRRLAMYCLKDAYLP
LRLLNKLMCIVNYMEMARVTGVSLASLLTRGQQIKVVSQLLRKARDAGYLIPTYTSQGGD
NEQFEGATVIEPKRGYYSVPIATLDFASLYPSIMMAHNLCYTTLLKPSDRKKLDLKDEDV
TQTPAGNFFVKPNVRKGLLPEILESLLSARKKAKADLKSETDPFKRSVLDGRQLALKISA
NSVYGFTGAQVGKLPCLEISGSVTAYGRTMIEMTKNEVEKKYTLSNGYDSDAFVIYGDTD
SVMVNFGTESLPRAMELGREAAEFVSEKFIKPIKLEFEKVYYPYLLINKKRYAGLYWTKP
ENYDKMDCKGIETVRRDNSPLVANLMNTCLQKLLIERNPTEAVDYVKSIISDLLCNRIDI
SQLVITKELTKHDYAAKQAHVELAAKMKKRDPGNAPKLGDRVPYVITASAKSTPAYQKAE
DPVYVLENSIPIDFQYYLDNQLSKPLLRIFEPILGDKAESILLRGDHTRTRMGGTSKVSA
LSAFVQRKETCIGCKSVLSADRSKGALCQHCETKSDEIYQNEIVQQCQLEERFSRLWAEC
QRCQGARNEEVLCTSRDCPIFYMRTKVRMDLDTQNKRIMRFGLSAINNW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g2005.t2 CDD cd05777 DNA_polB_delta_exo 1 194 2.17324E-128
16 g2005.t2 CDD cd05533 POLBc_delta 242 634 0.0
13 g2005.t2 Gene3D G3DSA:3.30.420.10 - 1 188 3.3E-77
14 g2005.t2 Gene3D G3DSA:1.10.287.690 Helix hairpin bin 189 237 5.6E-9
12 g2005.t2 Gene3D G3DSA:3.90.1600.10 Palm domain of DNA polymerase 244 473 1.4E-82
15 g2005.t2 Gene3D G3DSA:1.10.287.690 Helix hairpin bin 317 369 1.4E-82
11 g2005.t2 Gene3D G3DSA:1.10.132.60 - 490 643 1.2E-48
4 g2005.t2 PANTHER PTHR10322:SF23 DNA POLYMERASE DELTA CATALYTIC SUBUNIT 1 762 0.0
5 g2005.t2 PANTHER PTHR10322 DNA POLYMERASE CATALYTIC SUBUNIT 1 762 0.0
8 g2005.t2 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 261 274 8.2E-12
7 g2005.t2 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 353 365 8.2E-12
6 g2005.t2 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 414 422 8.2E-12
1 g2005.t2 Pfam PF03104 DNA polymerase family B, exonuclease domain 1 138 1.2E-33
2 g2005.t2 Pfam PF00136 DNA polymerase family B 204 633 2.2E-149
3 g2005.t2 Pfam PF14260 C4-type zinc-finger of DNA polymerase delta 671 744 6.1E-16
18 g2005.t2 ProSitePatterns PS00116 DNA polymerase family B signature. 416 424 -
19 g2005.t2 SMART SM00486 polmehr3 1 428 7.1E-139
10 g2005.t2 SUPERFAMILY SSF53098 Ribonuclease H-like 2 225 6.56E-61
9 g2005.t2 SUPERFAMILY SSF56672 DNA/RNA polymerases 228 641 1.89E-131
20 g2005.t2 TIGRFAM TIGR00592 pol2: DNA polymerase (pol2) 224 631 3.2E-86

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003887 DNA-directed DNA polymerase activity MF
GO:0003677 DNA binding MF
GO:0000166 nucleotide binding MF
GO:0003676 nucleic acid binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values